if (!require(devtools)) install.packages("devtools")
## Loading required package: devtools
## Loading required package: usethis
devtools::install_github("yanlinlin82/ggvenn")
## Skipping install of 'ggvenn' from a github remote, the SHA1 (335cfe1e) has not changed since last install.
##   Use `force = TRUE` to force installation

GeneSet Analysis

library(ggvenn)
## Loading required package: dplyr
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
## Loading required package: grid
## Loading required package: ggplot2
Kahraman_paths <- file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/GeneSets/Kahraman", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

Clemente_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/GeneSets/Clemente", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

Vitting_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/GeneSets/Vitting/", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

for (i in 1:9) {
  Kahraman = read.csv(Kahraman_paths[i], header = FALSE)
  Clemente = read.csv(Clemente_paths[i], header = FALSE)
  Vitting = read.csv(Vitting_paths[i], header = FALSE)
  Genelist <- list(
  Kahraman_Study = Kahraman$V1,
  Clemente_Study = Clemente$V1,
  Vitting_Study = Vitting$V1
  )

  print(ggvenn(
  Genelist, 
  fill_color = c("skyblue1", "#EFC000FF", "tomato1"),
  stroke_size = 0.3, set_name_size = 4,text_color = "black", text_size = 2
  ))
  
  print(intersect(intersect(Kahraman, Clemente), Vitting))
  }

##        V1
## 1     TNC
## 2   ATXN3
## 3  FAM76B
## 4    CAP2
## 5  PNPLA7
## 6    PPAN
## 7   DACH1
## 8   CPLX1
## 9    SKA2
## 10  BICD2
## 11  HOXC6

##            V1
## 1    C19orf60
## 2      OSBPL5
## 3        CD44
## 4     ZFYVE16
## 5        TLE2
## 6  ST6GALNAC1
## 7       LIMS2
## 8       CALD1
## 9        PNKD
## 10       SHC2
## 11       RIN2
## 12      MYO10
## 13    C7orf50
## 14        AK3
## 15    RABGEF1
## 16     TSPAN7
## 17      FMNL3
## 18       ING2
## 19       PCCA
## 20     SH3BGR
## 21     BTN3A2

##         V1
## 1     CD44
## 2    RC3H2
## 3  CEACAM1
## 4    NRCAM
## 5   CDADC1
## 6    GSPT1
## 7     CAV1
## 8    DNMBP
## 9     LIPA
## 10   NCOA7
## 11    KTN1
## 12  PDGFRA
## 13   BCAR3
## 14    RGS3
## 15   TARS2
## 16 ZNF385B
## 17   OBSCN
## 18    NAGS
## 19   BSCL2
## 20  PCMTD1
## 21   AP1S2
## 22    EXD3
## 23   ZNF44
## 24    WWP2
## 25  CTNND1
## 26  SCAMP5

##       V1
## 1  KIF22
## 2   NXT2
## 3   NT5E
## 4   GBAS
## 5  PANK1
## 6  CXADR
## 7  MFAP4
## 8  NUDT6
## 9   FGGY
## 10  AQP1

##          V1
## 1     SPAG9
## 2       LSR
## 3     ITM2C
## 4     CXADR
## 5     CPLX1
## 6 TNFRSF10C

##         V1
## 1   CASP10
## 2  SDCCAG8
## 3    ATXN3
## 4    CECR1
## 5   DYRK1B
## 6      LSR
## 7     MEST
## 8     GAB1
## 9    CNOT2
## 10   MKLN1
## 11 SHROOM2
## 12   NTRK2
## 13     DST
## 14  IL17RE
## 15 PPFIBP2
## 16    WWOX
## 17  CTNND1

##      V1
## 1 VAMP1

##         V1
## 1      CFH
## 2 C1orf198
## 3  FAM174B

##         V1
## 1  PLEKHH1
## 2    FGFR2
## 3    BAZ2A
## 4  SMARCA2
## 5    IPO11
## 6    CECR1
## 7    PATZ1
## 8     ASB9
## 9     FLT1
## 10   DOCK8
## 11   DNMBP
## 12   SHOC2
## 13     MVK
## 14    MXI1
## 15   ACOT9
## 16    PSD4
## 17  EPS8L1
## 18  PDGFRA
## 19    BIVM
## 20    CIB2
## 21    BIN1
## 22   BCAR3
## 23   NCOA4
## 24  RNF185
## 25   DCDC2
## 26  ZNF185
## 27  TM7SF2
## 28    SCOC
## 29   CXADR
## 30 RABGEF1
## 31 SLC35B2
## 32   KALRN
## 33 GOLGA8A
## 34 GRAMD1C
## 35   LIMK2
## 36   AFMID
## 37   RBM33
## 38    WWP2
## 39  SCAMP5

Isoform Switch Analysis

Kahraman_paths <- file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Kahraman", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

Clemente_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Clemente", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

Vitting_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Vitting/", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

for (i in 1:9) {
  Kahraman = read.csv(Kahraman_paths[i], header = TRUE)
  Clemente = read.csv(Clemente_paths[i], header = TRUE)
  Vitting = read.csv(Vitting_paths[i], header = TRUE)
  Genelist <- list(
  Kahraman_Study = Kahraman$Normal_Isoform_Cancer_Isoform,
  Clemente_Study = Clemente$Normal_Isoform_Cancer_Isoform,
  Vitting_Study = Vitting$Normal_Isoform_Cancer_Isoform
  )

  print(ggvenn(
  Genelist, 
  fill_color = c("skyblue1", "#EFC000FF", "tomato1"),
  stroke_size = 0.3, set_name_size = 4,text_color = "black", text_size = 2
  ))
  
  print(intersect(intersect(Kahraman, Clemente), Vitting))
  }

##   Normal_Isoform_Cancer_Isoform
## 1             uc003gbj_uc003gbi
## 2             uc004aso_uc004asp
## 3             uc003ncb_uc011djb

##   Normal_Isoform_Cancer_Isoform
## 1             uc002vhm_uc002vhq

##   Normal_Isoform_Cancer_Isoform
## 1             uc002otv_uc002otw
## 2             uc001mvx_uc001mvw
## 3             uc002unj_uc002unn

##   Normal_Isoform_Cancer_Isoform
## 1             uc003iew_uc003iex
## 2             uc003tbv_uc010kwf
## 3             uc003pko_uc010kbr
## 4             uc003tre_uc003trf
## 5             uc002yki_uc002ykj
## 6             uc001kgn_uc001kgo
## 7             uc001qyu_uc001qyt

##   Normal_Isoform_Cancer_Isoform
## 1             uc003gbj_uc003gbi
## 2             uc002yki_uc002ykj

##   Normal_Isoform_Cancer_Isoform
## 1             uc002uxj_uc010ftb
## 2             uc002nym_uc002nyn
## 3             uc003vqg_uc003vqc

## [1] Normal_Isoform_Cancer_Isoform
## <0 rows> (or 0-length row.names)

## [1] Normal_Isoform_Cancer_Isoform
## <0 rows> (or 0-length row.names)

##   Normal_Isoform_Cancer_Isoform
## 1             uc001kza_uc001kyy
## 2             uc003akb_uc003ake
## 3             uc002bdb_uc002bdc
## 4             uc002yki_uc002ykj
## 5             uc003aks_uc003akr
## 6             uc003eas_uc003eaq

Normal Isoform Analysis

library(tidyr)

Kahraman_paths <- file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch//Kahraman", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

Clemente_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Clemente", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

Vitting_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Vitting/", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

for (i in 1:9) {
  Kahraman = read.csv(Kahraman_paths[i], header = TRUE)
  
  Kahraman_Normals <- (Kahraman %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"),  "_"))[,1][2:length(Kahraman[,1])]
  
  Clemente = read.csv(Clemente_paths[i], header = TRUE)
  
  Clemente_Normals <- (Clemente %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"),  "_"))[,1][2:length(Clemente[,1])]
  
  Vitting = read.csv(Vitting_paths[i], header = TRUE)
  
  Vitting_Normals <- (Vitting %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"),  "_"))[,1][2:length(Vitting[,1])]
    
  Genelist <- list(
  Kahraman_Study = unique(Kahraman_Normals),
  Clemente_Study = unique(Clemente_Normals),
  Vitting_Study = unique(Vitting_Normals)
  )

  print(ggvenn(
  Genelist, 
  fill_color = c("skyblue1", "#EFC000FF", "tomato1"),
  stroke_size = 0.3, set_name_size = 4,text_color = "black", text_size = 2
  ))
  
  
  print(intersect(intersect(Kahraman_Normals, Clemente_Normals), Vitting_Normals))
  }

## [1] "uc003gbj" "uc004aso" "uc003ncb" "uc001sev"

##  [1] "uc002tpa" "uc001voo" "uc001lxk" "uc002njv" "uc002vhm" "uc002jsh"
##  [7] "uc003kgq" "uc002loq" "uc003jft" "uc003ziq" "uc004deg" "uc002yya"

##  [1] "uc002otv" "uc001qba" "uc004cxi" "uc004cmp" "uc001mvx" "uc001nup"
##  [7] "uc003vfc" "uc003han" "uc002unj" "uc002ies"

##  [1] "uc003iew" "uc003tbv" "uc002gvt" "uc003pko" "uc003tre" "uc002yki"
##  [7] "uc001kgn" "uc003hzc" "uc001qyu" "uc004eof"

## [1] "uc002vqz" "uc003gbj" "uc003xcy" "uc002yki"

## [1] "uc002uxj" "uc002nym" "uc002ffk" "uc004csu" "uc011chq" "uc009zro" "uc003vqg"
## [8] "uc003btw"

## character(0)

## [1] "uc001hub" "uc010boe"

##  [1] "uc001kzl" "uc009zvk" "uc001kza" "uc001vps" "uc002tob" "uc003akb"
##  [7] "uc001oct" "uc003oxd" "uc003vcm" "uc002zmj" "uc002bdb" "uc002yki"
## [13] "uc001xjl" "uc003han" "uc011che" "uc002jva" "uc003aks" "uc004cwk"
## [19] "uc004dap" "uc002tjc" "uc002qis" "uc003ndx" "uc003eas"

Cancer Isoform Analysis

library(tidyr)

Kahraman_paths <- file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch//Kahraman", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

Clemente_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Clemente", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

Vitting_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Vitting/", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))

for (i in 1:9) {
  Kahraman = read.csv(Kahraman_paths[i], header = TRUE)
  
  Kahraman_Cancer <- (Kahraman %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"),  "_"))[,2][2:length(Kahraman[,1])]
  
  Clemente = read.csv(Clemente_paths[i], header = TRUE)
  
  Clemente_Cancer <- (Clemente %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"),  "_"))[,2][2:length(Clemente[,1])]
  
  Vitting = read.csv(Vitting_paths[i], header = TRUE)
  
  Vitting_Cancer <- (Vitting %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"),  "_"))[,2][2:length(Vitting[,1])]
    
  Genelist <- list(
  Kahraman_Study = unique(Kahraman_Cancer),
  Clemente_Study = unique(Clemente_Cancer),
  Vitting_Study = unique(Vitting_Cancer)
  )

  print(ggvenn(
  Genelist, 
  fill_color = c("skyblue1", "#EFC000FF", "tomato1"),
  stroke_size = 0.3, set_name_size = 4,text_color = "black", text_size = 2
  ))
  
  
  print(intersect(intersect(Kahraman_Cancer, Clemente_Cancer), Vitting_Cancer))  
  }

## [1] "uc003gbi" "uc004asp" "uc002uhz" "uc011djb"

## [1] "uc003sju" "uc003tvh" "uc002uhz" "uc002vhq" "uc009xkg"

## [1] "uc002otw" "uc003qai" "uc001mvw" "uc001dpy" "uc002unn"

## [1] "uc003iex" "uc010kwf" "uc010kbr" "uc003trf" "uc002ykj" "uc001kgo" "uc001qyt"
## [8] "uc002dts"

## [1] "uc003gbi" "uc002ykj"

## [1] "uc010ftb" "uc002nyn" "uc003pdc" "uc003vqc"

## character(0)

## [1] "uc009xkg"

## [1] "uc001kyy" "uc003ake" "uc003tvh" "uc003ehk" "uc002bdc" "uc001dpy" "uc002ykj"
## [8] "uc003akr" "uc003eaq"